Mercurial > repos > iuc > ucsc_maftoaxt

changeset 1:a6540beef35f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt commit 303002db06287fb25306020c4391626842f52162
author iuc
date Sun, 22 Sep 2024 07:26:36 +0000
parents 3a4256d4f079
children
files maftoaxt.xml
diffstat 1 files changed, 8 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/maftoaxt.xml	Wed Jul 31 14:29:16 2024 +0000
+++ b/maftoaxt.xml	Sun Sep 22 07:26:36 2024 +0000
@@ -3,7 +3,7 @@
         Convert file from MAF to axt format
     </description>
     <macros>
-        <token name="@TOOL_VERSION@">377</token>
+        <token name="@TOOL_VERSION@">469</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
@@ -25,7 +25,7 @@
             $stripDb
         ]]></command>
         <inputs>
-            <param name="in_maf" format="maf" type="data" label="maf file" />
+            <param name="in_maf" format="maf" type="data" label="MAF dataset" />
 
             <conditional name="tar_seq">
                 <param name="tarSeq" type="select" label="Select target sequence" optional="false" help="Which sequence from the MAF file should be used as the target sequence. ">
@@ -62,9 +62,14 @@
         <help><![CDATA[
     **What it does**
 
-    `mafToAxt`_ is a tool to convert maf dataset to axt format. Depending on parameters and the number of alignments in the MAF file this can be a full conversion or data extraction.
+    `mafToAxt`_ is a tool to convert `MAF`_ dataset to `axt`_ format. Depending on parameters and the number of alignments in the MAF file this can be a full conversion or data extraction.
+
+    For implementation details see mafToAxt's `source code`_.
 
     .. _mafToAxt: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+    .. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
+    .. _MAF: https://genome.ucsc.edu/FAQ/FAQformat.html#format5
+    .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/mafToAxt/mafToAxt.c
         ]]>    </help>
         <citations>
             <citation type="doi">10.1093/bib/bbs038</citation>